Publication

The eukaryotic promoter database (EPD)

Related concepts (33)

Graph Chatbot

Chat with Graph Search

Ask any question about EPFL courses, lectures, exercises, research, news, etc. or try the example questions below.

DISCLAIMER: The Graph Chatbot is not programmed to provide explicit or categorical answers to your questions. Rather, it transforms your questions into API requests that are distributed across the various IT services officially administered by EPFL. Its purpose is solely to collect and recommend relevant references to content that you can explore to help you answer your questions.

Comparative genomics

Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms.

Document-oriented database

A document-oriented database, or document store, is a computer program and data storage system designed for storing, retrieving and managing document-oriented information, also known as semi-structured data. Document-oriented databases are one of the main categories of NoSQL databases, and the popularity of the term "document-oriented database" has grown with the use of the term NoSQL itself. XML databases are a subclass of document-oriented databases that are optimized to work with XML documents.

Object–relational database

An object–relational database (ORD), or object–relational database management system (ORDBMS), is a database management system (DBMS) similar to a relational database, but with an object-oriented database model: objects, classes and inheritance are directly supported in database schemas and in the query language. In addition, just as with pure relational systems, it supports extension of the data model with custom data types and methods. An object–relational database can be said to provide a middle ground between relational databases and object-oriented databases.

Functional genomics

Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects (such as genome sequencing projects and RNA sequencing). Functional genomics focuses on the dynamic aspects such as gene transcription, translation, regulation of gene expression and protein–protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures.

GenBank

The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States) as part of the International Nucleotide Sequence Database Collaboration (INSDC). GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 500,000 formally described species.

Gene prediction

In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms.

Multiple sequence alignment

Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins.

Common Gateway Interface

In computing, Common Gateway Interface (CGI) is an interface specification that enables web servers to execute an external program to process HTTP/S user requests. Such programs are often written in a scripting language and are commonly referred to as CGI scripts, but they may include compiled programs. A typical use case occurs when a web user submits a web form on a web page that uses CGI. The form's data is sent to the web server within an HTTP request with a URL denoting a CGI script.

Vector (molecular biology)

In molecular cloning, a vector is any particle (e.g., plasmids, cosmids, Lambda phages) used as a vehicle to artificially carry a foreign nucleic sequence – usually DNA – into another cell, where it can be replicated and/or expressed. A vector containing foreign DNA is termed recombinant DNA. The four major types of vectors are plasmids, viral vectors, cosmids, and artificial chromosomes. Of these, the most commonly used vectors are plasmids. Common to all engineered vectors are an origin of replication, a multicloning site, and a selectable marker.

Database scalability

Database scalability is the ability of a database to handle changing demands by adding/removing resources. Databases use a host of techniques to cope. The initial history of database scalability was to provide service on ever smaller computers. The first database management systems such as IMS ran on mainframe computers. The second generation, including Ingres, Informix, Sybase, RDB and Oracle emerged on minicomputers. The third generation, including dBase and Oracle (again), ran on personal computers.